SCANPY: large-scale single-cell gene expression data analysis
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TLDR
This work presents Scanpy, a scalable toolkit for analyzing single-cell gene expression data that includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks, and AnnData, a generic class for handling annotated data matrices.Abstract:
Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks. Its Python-based implementation efficiently deals with data sets of more than one million cells (
https://github.com/theislab/Scanpy
). Along with Scanpy, we present AnnData, a generic class for handling annotated data matrices (
https://github.com/theislab/anndata
).read more
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Dimensionality reduction for visualizing single-cell data using UMAP.
Etienne Becht,Leland McInnes,John Healy,Charles-Antoine Dutertre,Immanuel Kwok,Lai Guan Ng,Florent Ginhoux,Evan W. Newell,Evan W. Newell +8 more
TL;DR: Comparing the performance of UMAP with five other tools, it is found that UMAP provides the fastest run times, highest reproducibility and the most meaningful organization of cell clusters.
Journal ArticleDOI
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.
Waradon Sungnak,Ni Huang,Christophe Bécavin,Marijn Berg,Rachel Queen,Monika Litvinukova,Monika Litvinukova,Carlos Talavera-López,Henrike Maatz,Daniel Reichart,Fotios Sampaziotis,Kaylee B Worlock,Masahiro Yoshida,Josephine Barnes +13 more
TL;DR: In this paper, the expression of viral entry-associated genes in single-cell RNA-sequencing data from multiple tissues from healthy human donors was investigated, and co-detected these transcripts in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission.
Journal ArticleDOI
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.
Carly G. K. Ziegler,Samuel J. Allon,Sarah K. Nyquist,Ian M. Mbano,Vincent N. Miao,Constantine N. Tzouanas,Yuming Cao,Ashraf S. Yousif,Julia Bals,Blake M. Hauser,Blake M. Hauser,Jared Feldman,Jared Feldman,Christoph Muus,Christoph Muus,Marc H. Wadsworth,Samuel W. Kazer,Travis K. Hughes,Benjamin Doran,G. James Gatter,G. James Gatter,G. James Gatter,Marko Vukovic,Faith Taliaferro,Faith Taliaferro,Benjamin E. Mead,Zhiru Guo,Jennifer P. Wang,Delphine Gras,Magali Plaisant,Meshal Ansari,Ilias Angelidis,Heiko Adler,Jennifer M.S. Sucre,Chase J. Taylor,Brian M. Lin,Avinash Waghray,Vanessa Mitsialis,Vanessa Mitsialis,Daniel F. Dwyer,Kathleen M. Buchheit,Joshua A. Boyce,Nora A. Barrett,Tanya M. Laidlaw,Shaina L. Carroll,Lucrezia Colonna,Victor Tkachev,Victor Tkachev,Christopher W. Peterson,Christopher W. Peterson,Alison Yu,Alison Yu,Hengqi Betty Zheng,Hengqi Betty Zheng,Hannah P. Gideon,Caylin G. Winchell,Philana Ling Lin,Philana Ling Lin,Colin D. Bingle,Scott B. Snapper,Scott B. Snapper,Jonathan A. Kropski,Jonathan A. Kropski,Fabian J. Theis,Herbert B. Schiller,Laure-Emmanuelle Zaragosi,Pascal Barbry,Alasdair Leslie,Alasdair Leslie,Hans-Peter Kiem,Hans-Peter Kiem,JoAnne L. Flynn,Sarah M. Fortune,Sarah M. Fortune,Sarah M. Fortune,Bonnie Berger,Robert W. Finberg,Leslie S. Kean,Leslie S. Kean,Manuel Garber,Aaron G. Schmidt,Aaron G. Schmidt,Daniel Lingwood,Alex K. Shalek,Jose Ordovas-Montanes,Nicholas E. Banovich,Alvis Brazma,Tushar J. Desai,Thu Elizabeth Duong,Oliver Eickelberg,Christine S. Falk,Michael Farzan,Ian A. Glass,Muzlifah Haniffa,Peter Horvath,Deborah T. Hung,Naftali Kaminski,Mark A. Krasnow,Malte Kühnemund,Robert Lafyatis,Haeock Lee,Sylvie Leroy,Sten Linnarson,Joakim Lundeberg,Kerstin B. Meyer,Alexander V. Misharin,Martijn C. Nawijn,Marko Nikolic,Dana Pe'er,Joseph E. Powell,Stephen R. Quake,Jay Rajagopal,Purushothama Rao Tata,Emma L. Rawlins,Aviv Regev,Paul A. Reyfman,Mauricio Rojas,Orit Rosen,Kourosh Saeb-Parsy,Christos Samakovlis,Herbert B. Schiller,Joachim L. Schultze,Max A. Seibold,Douglas P. Shepherd,Jason R. Spence,Avrum Spira,Xin Sun,Sarah A. Teichmann,Fabian J. Theis,Alexander M. Tsankov,Maarten van den Berge,Michael von Papen,Jeffrey A. Whitsett,Ramnik J. Xavier,Yan Xu,Kun Zhang +135 more
TL;DR: The data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection.
Journal ArticleDOI
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
TL;DR: It is proposed that the Pearson residuals from “regularized negative binomial regression,” where cellular sequencing depth is utilized as a covariate in a generalized linear model, successfully remove the influence of technical characteristics from downstream analyses while preserving biological heterogeneity.
Journal ArticleDOI
The single-cell transcriptional landscape of mammalian organogenesis
Junyue Cao,Malte Spielmann,Xiaojie Qiu,Xingfan Huang,Daniel M. Ibrahim,Daniel M. Ibrahim,Andrew J. Hill,Fan Zhang,Stefan Mundlos,Stefan Mundlos,Lena Christiansen,Frank J. Steemers,Cole Trapnell,Jay Shendure +13 more
TL;DR: A cell atlas of mouse organogenesis provides a global view of developmental processes occurring during this critical period, including focused analyses of the apical ectodermal ridge, limb mesenchyme and skeletal muscle.
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